Heavy ions refer to charged particles with a mass greater than four (i.e., alpha particles). The heavy ion irradiation used in radiotherapy or that astronauts suffer in space flight missions induces toxicity in normal tissue and leads to short-term and long-term damage in both the structure and function of the brain. However, the underlying molecular alterations caused by heavy ion radiation have yet to be completely elucidated. Herein, untargeted and targeted lipidomic profiling of the whole brain tissue and blood plasma 7 days after the administration of the 15 Gy (260 MeV, low linear energy (LET) = 13.9 KeV/μm) plateau irradiation of disposable 12C6+ heavy ions on the whole heads of rats was explored to study the lipid damage induced by heavy ion radiation in the rat brain using ultra performance liquid chromatography-mass spectrometry (UPLC-MS) technology. Combined with multivariate variables and univariate data analysis methods, our results indicated that an orthogonal partial least squares discriminant analysis (OPLS-DA) could clearly distinguish lipid metabolites between the irradiated and control groups. Through the combination of variable weight value (VIP), variation multiple (FC), and differential (p) analyses, the significant differential lipids diacylglycerols (DAGs) were screened out. Further quantitative targeted lipidomic analyses of these DAGs in the rat brain tissue and plasma supported the notion that DAG 47:1 could be used as a potential biomarker to study brain injury induced by heavy ion irradiation.